Journal of the Association of Genetic Technologists最新文献

Objectives: The Janus Kinase 2 gene (JAK2) provides instructions for generating a protein that promotes the division and growth, or what is referred to as the proliferation, of cells. This generated protein relays signals in cells in order to promote cell growth, as well as help manage the count of white blood cells, red blood cells, and platelets that are generated within the bone marrow. Mutations and rearrangements of JAK2 are found in 3.5% of B-acute lymphoblastic leukemia (B-ALL) cases and in 18.9% of Down syndrome B-ALL patients, and are associated with a Ph-like ALL and a poor prognosis. However, there have been great challenges in understanding their role in this pathogenesis. In this review, we will discuss the most recent literature and trends associated with JAK2 mutations in patients with B-ALL.

Objectives: The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.

Objectives: A recent landmark study reported the value of next-generation sequencing (NGS) to uncover pathogenic abnormalities of clinical significance in patients with pediatric B-ALL enrolled in the UKALL2003 clinical trial (Schwab et al., 2023). NGS, as whole genome sequencing (WGS) or targeted NGS (t-NGS), was combined with previous data (cytogenetics, FISH and MLPA) from 351 pediatric patients with precursor B-ALL who lacked a defining genetic abnormality (B-other ALL). This integration of tests classified patients into 15 distinct subtypes, each one characterized by a specific abnormality. The most frequent subtypes were defined by abnormalities of PAX5, DUX4, ZNF384, an ABL class, and an ETV6::RUNX1-like with a gene expression profile similar to the typical ETV6::RUNX1 but without the specific abnormality. Quite conspicuously, WGS detected some classical abnormalities that remained undetected by standard cytogenomic methods. This application of NGS integrated into standard cytogenomic assays is a decisive advance in classifying patients with B-other ALL into distinct subtypes characterized by unique genomic changes. The addition of NGS improved the identification of pathogenic abnormalities and refined the classification as well as the risk stratification to determine clinical prognosis.

Objectives: Congenital neutropenia, defined by absolute neutrophil count (ANC) 2.5x109/L in infants, includes a variety of genotypic alterations that manifest with chronic immunodeficiency and, as a result, presents in infancy with recurrent infections. The gene that encodes neutrophil elastase, ELANE, has pathological variants yielding two distinct phenotypes: severe congenital neutropenia (SCN) and cyclic neutropenia (CyN). While SCN exhibits persistent pathologic ANC values, CyN exhibits pathologic ANC values in a patterned fashion which can recur in 21-day intervals. Here, we describe a patient with a novel heterozygous ELANE deletion (c.224+(4_19)del16) presenting with clinical features consistent with CyN and a response to first-line therapy of granulocyte colony- stimulating factor.

Objectives: The latest study with whole genome sequencing (WGS) in pediatric B-ALL validated its use as a standalone test to detect underlying clinically significant genetic abnormalities (Rezayee et al., 2023). This was a retrospective molecular survey in bone marrows previously collected and stored from 88 patients who were enrolled in NOPHO trials. The testing was done through 150 bp paired-end WGS applied to a paired analysis of leukemia-germline samples (L-N) (n=64), and to the analysis of leukemia-only samples (L) (n=88). The results demonstrated a full concordance between both WGS approaches and between the results from WGS and previous standard of care tests (SOCTs). All the mandatory aberrations that require testing in the current ALLTogether trial protocol were identified in 38 patients. In addition, WGS accurately identified the majority of aberrations characteristic of B-other ALL (35/36 cases), copy number abnormalities (CNAs) in eight critical genes or regions, CNAs that characterize the IKZF1plus profile, and the abnormalities in patients with Down syndrome. An adapted methodology was necessary for the detection of DUX4::IGH rearrangements in four patients. A comparison between sequencing coverages of 90X and 30X demonstrated that a lower 30X coverage was sufficient to detect all the relevant abnormalities. This successful testing was accomplished through filtering of WGS data focusing on just genes and genomic regions that are routinely implicated in pediatric B-ALL. As a result, it simplified the extraction of data and facilitated the interpretation of results. Overall, the precise identification of abnormalities that was accomplished by WGS allowed the assignment of patients to distinct genetic subtypes. The conclusion of this study was that WGS is quite reliable and can replace the use of SOCTs to profile pediatric B-ALL.

Objectives: A new study demonstrated the power of WGS to comprehensively and accurately profile the genetic abnormalities in cases of childhood B-ALL that were previously studied with standard cytogenetics, FISH and MLPA (Ryan et al., 2023). Two cohorts with a total of 210 patients were studied. One cohort carried cytogenetic abnormalities of known significance (n=38). The other cohort (n=172) lacked cytogenetic abnormalities detectable by standard methods (B-other ALL group), and was treated within the UKALL2003 clinical trial. The WGS approaches used were a tumor-normal (T-N) pipeline and a tumor-only (T-only) pipeline. Most patients (202/210) carried a distinct abnormality already known or a new one that defined a genetic subtype. WGS identified almost all the abnormalities in the cohort with typical cytogenetic abnormalities previously detected (37/38 in the T-only pipeline, 34/38 in the T-N pipeline). The B-other ALL cohort showed two types of abnormalities by WGS. Some were cytogenetic abnormalities emblematic of B-ALL that were missed by previous standard methods (19/172 cases) due to poor samples or incomplete testing at the time of diagnosis. The remaining abnormalities were cryptic (145/153 cases) and defined genetic subtypes. Some new molecular variants emerged with WGS, the profile of PAX5 rearrangements and the ETV6::RUNX1-like subtype was characterized in more detail, and the detection of DUX4 rearrangements was markedly improved by a novel bioinformatic pipeline. Whole transcriptome sequencing (WTS) conducted in a subset of 85 patients was consistent with the results of WGS and standard cytogenomic techniques. This study validated the diagnostic use of WGS to uncover and characterize in detail the genetic aberrations in pediatric B-ALL. As a result, Ryan et al. endorsed the routine use of WGS to discover more abnormalities of clinical significance that define new genetic subtypes, as well as to improve diagnosis, risk stratification, and therapy.

Objectives: B-cell acute lymphoblastic leukemia (B-ALL) is one of the most common leukemias affecting the pediatric population. It represents ~25% of cancer diagnoses among children. Specific genetic changes predict the prognosis in B-ALL with recurrent genetic changes. Here we present a case report of a 20-year-old male with B-ALL. The patient presented with acute onset worsening upper extremity pain with pallor, weight loss, dizziness, fatigue, and abnormal complete blood count (CBC). Conventional cytogenetics showed a karyotype of 46,XY,add(9)(q13),i(9)(q10)[19]. DNA FISH analysis performed on the bone marrow showed hemizygous deletion of the 9p21(CDKN2A) in 15.5% of the nuclei examined. The presence of an isochromosome 9q [i(9)(q10) is a rare event in pediatric B-ALL. An isochromosome 9q occurs in 0.6% of the patients studied in the literature. The significance of this abnormality in pediatric B-ALL is not clear. Profiling cases like this to understand the molecular mechanisms of rare chromosomal abnormalities and rare mutations in children with B-ALL could help us to better treat them.

Objectives: Noninvasive prenatal testing (NIPT) has become a widely used screening method to detect fetal aneuploidies using cell-free fetal DNA (cffDNA) obtained from maternal blood. It is noninvasive, highly sensitive and specific, and can be offered in the first trimester of pregnancy. Though the goal of NIPT is to detect abnormalities in fetal DNA, occasionally abnormalities are detected that are not attributable to the fetus. Tumor DNA is laden with abnormalities and, rarely, NIPT has detected occult malignancy in the mother. Maternal malignancy in pregnancy is relatively uncommon, estimated at 1 in 1,000 pregnant women. We present a case of a 38-year-old woman diagnosed with multiple myeloma after abnormal NIPT testing results.

Objectives: Chronic lymphocytic leukemia (CLL) is a malignancy identified by an increase in the number of lymphocytes in the blood. It is one of the most common adult leukemias. It is a heterogeneous clinical disease with changeable progression. Chromosomal aberrations play a significant role in predicting clinical outcomes and survival. Treatment strategies for each patient are determined by chromosomal abnormalities. Cytogenetic methods are sensitive procedures for detecting abnormalities in the genome. The aim of this study was to document the incidence of different genes and gene rearrangements in CLL patients by comparing conventional cytogenetic and fluorescence in situ hybridization (FISH) results and predicting their prognosis. Materials and Methods A total of 23 CLL patients, 18 men and five women with ages ranging from 45-75 years were enrolled in this case series. Interphase fluorescent in situ hybridization (I-FISH) was conducted on peripheral blood or bone marrow samples, whichever were available, and were cultured in growth culture medium. I-FISH was used to detect chromosomal abnormalities such as 11q-, del13q14, 17p-, 6q- and trisomy 12 in CLL patients. Results FISH results showed that there were different chromosomal gene rearrangements including del13q, del17p, del6q, del11q, and trisomy 12. Recurrent chromosomal abnormalities involved trisomy 12, del17p, del13q and novel translocation (8;17) were only seen in one patient. Conclusion Genomic aberrations in CLL are important independent predictors of disease progression and survival. Interphase cytogenetic analysis using FISH revealed chromosomal changes in the majority of CLL samples and is superior to standard karyotype analysis for identifying cytogenetic abnormalities.

Objectives: B-cell acute lymphoblastic leukemia (B-ALL) can afflict both adult and pediatric patients and is characterized by a build-up of B lymphoblasts. Here we present a case of a 25-year-old male patient with a history of B-ALL. Ninety percent of the bone marrow revealed pancytopenia with sheets of B lymphoblasts consistent with the diagnosis of B-ALL for acute pre-B lymphoblastic leukemia. The immunophenotype also presented predominant immature precursor B lymphoid cells positive for CD19, CD10, CD34, CD58, CD38, CD9, and TdT. Chromosome analysis of the bone marrow showed a complex karyotype described as 45~47,XY,i(8)(q10),der(10)add(10)(p11.1)add(10)(q23),-20,+1~2mar[cp3]/46,XY[36]. While IGH rearrangements were cryptic cytogenetically, DNA FISH analysis showed evidence of the IGH (14q32.2) gene rearrangement in 96.5% of the nuclei examined. These results were described as nuc ish(IGHx2)(5'IGH sep 3'IGHx1)[187/200],(5'IGH,3'IGH)x1~4(5'IGH con 3'IGHx0~2) [6/200]. The remaining probes were normal. Further studies using the MYC/IGH DC, DF probe from Abbott showed a gain of IGH signal in 7.5% of the nuclei examined: nuc ish(MYCx2,IGHx3)[15/200]. Metaphase FISH also showed that what appeared to be an isochromosome 8q was a derivative chromosome 8 defined as add(8)(p11.2) that contained a green IGH signal. In light of these results the karyotype was characterized as 45~47,XY,add(8)(p11.2),der(10)add(10)(p11.1)add(10)(q23),-20,+1~2mar[cp3].ish add(8) (p11.2) IgH+. IgH abnormalities are rare in B-ALL and are usually associated with a poor prognosis. However, at the present time our patient presented no evidence of persistent or residual disease and a cytogenetic response to the present therapy.